Merge pull request CEMeNT-PSAAP#145 from jpmorgan98/main

Testing Refactor, New Documentaiton, & Cont Energy Xsec Config script

.github/workflows/mpi_numba_reg.yml

@@ -0,0 +1,36 @@
+name: Regression Test - Numba and MPI
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest", "macos-latest"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: debug
+      run: |
+        pwd
+        ls
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        #sudo apt-get install libopenmpi-dev
+        pip install numpy numba h5py matplotlib scipy pytest colorama mpi4py ngsolve distinctipy
+        pip list 
+        pip install -e .
+    - name: Patch Numba
+      run : |
+        bash .github/workflows/patch.sh
+    - name: Regression Test - Numba and MPI
+      run: |
+          cd test/regression
+          python run.py --mode=numba --mpiexec=4
+          python run.py --mode=numba --mpiexec=2

.github/workflows/tests.yml → .github/workflows/mpi_reg.yml

@@ -1,10 +1,14 @@
-name: test
+name: Regression Test - MPI
 
 on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest", "macos-latest"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up python 3.11
@@ -25,26 +29,8 @@ jobs:
     - name: Patch Numba
       run : |
         bash .github/workflows/patch.sh
-    - name: Unit Test
-      run: |
-        pytest
-    - name: Regression Test - Python
-      run: |
-        cd test/regression
-        python run.py
     - name: Regression Test - MPI
       run: |
         cd test/regression
         python run.py --mpiexec=4
-        python run.py --mpiexec=2
-    - name: Regression Test - Numba
-      run: |
-        cd test/regression
-        python run.py --mode=numba
-    - name: Regression Test - Numba and MPI
-      run: |
-        cd test/regression
-        python run.py --mode=numba --mpiexec=4
-        python run.py --mode=numba --mpiexec=2
-    # TODO: Performance test
-    # TODO: GPU test
+        python run.py --mpiexec=2

.github/workflows/numba_reg.yml

@@ -0,0 +1,35 @@
+name: Regression Test - Numba
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: debug
+      run: |
+        pwd
+        ls
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        #sudo apt-get install libopenmpi-dev
+        pip install numpy numba h5py matplotlib scipy pytest colorama mpi4py ngsolve distinctipy
+        pip list 
+        pip install -e .
+    - name: Patch Numba
+      run : |
+        bash .github/workflows/patch.sh
+    - name: Regression Test - Numba
+      run: |
+          cd test/regression
+          python run.py --mode=numba

.github/workflows/python_reg.yml

@@ -0,0 +1,35 @@
+name: Regression Test - Python
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: debug
+      run: |
+        pwd
+        ls
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        #sudo apt-get install libopenmpi-dev
+        pip install numpy numba h5py matplotlib scipy pytest colorama mpi4py ngsolve distinctipy
+        pip list 
+        pip install -e .
+    - name: Patch Numba
+      run : |
+        bash .github/workflows/patch.sh
+    - name: Regression Test - Python
+      run: |
+          cd test/regression
+          python run.py

.github/workflows/unit_tests.yml

@@ -0,0 +1,34 @@
+name: Unit Test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: debug
+      run: |
+        pwd
+        ls
+    - uses: mpi4py/setup-mpi@v1
+    - name: Install dependencies
+      run: |
+        #sudo apt-get install libopenmpi-dev
+        pip install numpy numba h5py matplotlib scipy pytest colorama mpi4py ngsolve distinctipy
+        pip list 
+        pip install -e .
+    - name: Patch Numba
+      run : |
+        bash .github/workflows/patch.sh
+    - name: Unit Test
+      run : |
+          pytest

.gitignore

@@ -3,6 +3,10 @@ build
 .eggs
 mcdc.egg-info
 
+# Material Data
+mcdc_xs
+MCDC-Xsec
+
 # Python cache
 __pycache__
 *.pyc

CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
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+
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+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

README.md

@@ -10,7 +10,7 @@ MC/DC is a performant, scalable, and machine-portable Python-based Monte Carlo
 neutron transport software currently developed in the Center for Exascale Monte 
 Carlo Neutron Transport ([CEMeNT](https://cement-psaap.github.io/)).
 
-*Please Note that this project is in the early stages of devlopment (not even an alpha).* That being said enjoy!
+*Please Note that this project is in the early stages of devlopment.* We welcome any and all collaborators, feel free to reach out via comments or submit a PR! Enjoy!
 
 ## Installation
 

config_cont_energy.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+echo "WARNING: Seamless continous energy functionality"
+echo "is only avlible to CEMeNT members."
+echo " "
+
+# downloading library from zenodo
+git clone git@github.com:CEMeNT-PSAAP/MCDC-Xsec.git
+
+cd MCDC-Xsec
+
+# untaring file
+tar -xvzf mcdc_xs.tar.gz
+
+# going into the cross section library directory
+cd mcdc_xs
+
+# getting the present working direcotry
+xsec_dir=$(pwd)
+
+# exporting the needed enviroment variable for current enviroment
+export MCDC_XSLIB="${xsec_dir}"
+
+# adding that enviroment variable to bashrc for future runs
+export MCDC_XSLIB="${xsec_dir}">> ~/.bashrc 
+
+# printing a complete message
+echo "MCDC_XSLIB set as $MCDC_XSLIB in ~/.bashrc"